crossing96/oncoscreening huggingface dataset:
THRESHOLD: a comprehensive transcriptomic analysis tool for evaluating gene saturation and impact in disease progression.	Gene expression studies are fundamental in molecular biology, offering insights into development, disease progression, and therapeutic targets. To address the need for precise analysis of large datasets, we developed THRESHOLD, a novel tool that introduces the concept of gene saturation. Unlike traditional methods focused on absolute or binary expression levels, THRESHOLD quantifies the consistency of gene expression across patients, revealing co-regulation patterns critical for understanding disease mechanisms and stratifying patients by molecular signatures. The tool offers several features, including user-defined parameters, statistical comparisons, and interactive data visualization. THRESHOLD has uncovered compelling insights into disease progression using TCGA cancer datasets. For instance, bladder urothelial carcinoma demonstrated increasing upregulated gene saturation in progressive cancer stages (P < .00001). Moreover, THRESHOLD identified heightened gene saturation in patients with earlier onset of prostate adenocarcinoma (P < .0001) and revealed a critical fusion transcript, SLC45A2-AMACR, implicated in prostate adenocarcinoma progression, recurrence, and metastasis. Additionally, novel biomarkers and potential candidates for drug therapies were identified through protein-protein interaction networks and functional analyses of saturation data in colon adenocarcinoma and breast invasive carcinoma. THRESHOLD offers a new approach for studying gene expression dynamics and patient stratification. The tool is publicly available at Zenodo: https://zenodo.org/records/15287195.	bladder
Indoxyl sulfate promoted glutamine metabolism and cell proliferation in urothelial carcinoma involving Runx2.	Patients with Chronic Kidney Disease (CKD) have an increased risk and poor prognosis of becoming diagnosed with urothelial carcinoma. Currently, the linking mechanisms underlying the connection between CKD and urothelial carcinoma are not well understood. CKD with declined renal function is associated with the accumulation of circulating indoxyl sulfate, a metabolite synthesized from tryptophan by gut microbes. We investigated the roles of CKD-related uremic toxins in regards to their linking with urothelial carcinoma by delivering indoxyl sulfate to urothelial carcinoma cells and tumor-bearing mice. Upon exposure to indoxyl sulfate, urothelial carcinoma T24 and NTUB1 cells increased proliferation, accompanied by enhanced glutamine uptake and metabolism. Mechanistically, Runt-Related Transcription Factor 2 (Runx2) had been identified as a contributor of both urothelial carcinoma cell proliferation and Solute Carrier Family 1 Member 5 (SLC1A5)-mediated glutamine uptake, while metabolism was demonstrated as being a target to the actions of Runx2 promoted by indoxyl sulfate. An elevated expression of Runx2 caused by indoxyl sulfate correlated with both a reduction of microRNA-204 and an induction of DNA Methyltransferase 1 (DNMT1). MicroRNA-204 agomiR decreased Runx2 expression, while DNMT1 inhibitors reversed indoxyl sulfate-induced reduction of miR-204 and induction of Runx2. Additionally, inhibition of the Aryl Hydrocarbon Receptor (AhR) alleviated indoxyl sulfate-induced signaling changes and cell proliferation. The cancer-promoting effects of indoxyl sulfate were further demonstrated in tumor-bearing mice. In short, our results suggest that indoxyl sulfate may act as a bridge in linking the gap between CKD and urothelial carcinoma by involving the enhancement of glutamine uptake and metabolism.	bladder
Pathogenic Germline Variant Prevalence and Genetic Testing Outcomes in Patients With Urothelial Carcinoma.	INTRODUCTION: Urothelial carcinoma (UC) is rarely attributed to hereditary causes, but recent studies suggest inherited factors may play a larger role. Current guidelines recommend genetic evaluation in patients with UC diagnosed at < 50 years old or features associated with Lynch syndrome. However, the full pathogenic germline variant landscape and optimal genetic evaluation criteria in UC remain poorly understood. PATIENTS AND METHODS: A retrospective analysis of all patients with UC referred for genetic evaluation between 2002 and 2024 was performed. Genetic testing outcomes, variant prevalence and characterization, and associated clinicopathologic features were recorded. Fisher's Exact test was used to compare factors between patients with pathogenic or likely pathogenic (P/LP) variant versus those with negative testing. RESULTS: Overall, 128 patients underwent genetic evaluation. Median age at diagnosis was 59 (IQR: 48-68). Most (58.6%) had non-muscle invasive disease at initial diagnosis; 8.6% had metastatic disease. Pure urothelial histology was most frequent (71%). Upper tract disease was present at 14.8%. Among the cohort, 34 (26.6%) had a confirmed P/LP variant. The most common P/LP variants were Lynch syndrome-associated genes (9.4%) and DNA damage repair genes (9.4%). Having a history of ≥ 2 additional cancers was associated with a positive genetic test (P = .010). Otherwise, there were no statistically significant differences in testing outcomes based on age at diagnosis, primary tumor location, or initial stage at diagnosis. CONCLUSION: Among patients with UC referred for genetic evaluation, 26.6% had a confirmed P/LP variant, although this cohort was a selected population. Age and traditional clinicopathologic features were not associated with testing results, though history of ≥ 2 additional cancers was associated. These findings may suggest a broader use of genetic evaluation in UC.	bladder
Macrophage Cell and Diagnostic Biomarkers in BLCA: Integrating Machine Learning With Single-Cell Analysis.	INTRODUCTION: Bladder cancer (BLCA) has a poor prognosis and continues to pose a significant challenge for clinicians. Prior studies have demonstrated a close relationship of BLCA with macrophages. However, the key subpopulations and molecular functions of macrophages in BLCA have not been uncovered. It becomes possible to use single-cell sequencing technology to explore macrophage heterogeneity and identify new biomarkers. PATIENTS AND METHODS: Single-cell analysis, pseudo-time analysis, and cell-to-cell communication analysis were performed using single-cell sequencing data of PBMC, BLCA, and urothelial-derived cells (UDCs) obtained from the Gene Expression Omnibus (GEO). Scale-free network analysis was performed using hdWGCNA to select feature genes. LASSO regression and random forest analysis were performed based on TCGA_BLCA data. A prognostic model was established, which was then validated using the Gene Expression Omnibus (GEO) dataset. In addition, immune infiltration analysis was performed between high-risk and low-risk groups using the CIBERSORT, ESTIMATE algorithms, and the TIDE database. RESULTS: Nine macrophage subtypes were identified through single-cell analysis. 571 macrophage-associated genes were identified via hdWGCNA. Seven key genes, including MYO5A, KCNK6, DNAJB4, DEDD2, NFKBID, PSMB10, and ITPRID2, were selected by integrating LASSO regression and RF analysis. A prognostic model was constructed based on these genes. The high-risk cohort displayed markedly poorer overall survival (OS). The model's prediction accuracy was verified in an independent group. Immune analysis revealed enhanced immune evasion in the high-risk cohort, potentially facilitating tumor progression and increasing the metastatic capacity of BLCA cells. CONCLUSIONS: The prognostic model built on 7 macrophage-linked genes exhibited robust prediction performance in BLCA. The M2 macrophage phenotype was notably enriched in the high-risk cohort and appeared to cause elevated tumor invasiveness. Immune infiltration analysis suggested that the high-risk population showed a weaker response to immune checkpoint inhibitor (ICI) treatment. Among all identified genes, DEDD2 may serve as a promising prognostic biomarker for BLCA.	bladder
REV3L as a prognostic biomarker and therapeutic target in bladder urothelial carcinoma.	BACKGROUND: The functional significance and clinical relevance of the translesion DNA synthesis polymerase subunit REV3L in bladder urothelial carcinoma (BLCA) require comprehensive characterization. METHODS: Bioinformatic analysis of TCGA and GEO datasets was integrated with extensive experimental validation. The expression of REV3L was evaluated across various stages of BLCA, and its correlation with patient survival was analyzed using Kaplan-Meier analysis and Cox regression modelling. Additionally, immune infiltration patterns and pathway enrichment levels were investigated using GSEA. The functional consequences of REV3L depletion (shRNA) were evaluated in UMUC3 and SW780 cells through a series of assays for proliferation, colony formation, glycolysis (lactate production, glucose uptake, and gene expression), and cisplatin sensitivity (CCK-8 and apoptosis). RESULTS: REV3L expression was significantly lower in BLCA tumors than in normal tissues but higher in advanced-stage and high-grade tumors. High REV3L expression was found to be a strong predictor of poor overall survival, disease-specific survival, and progression-free interval. Furthermore, multivariate analysis revealed that high REV3L expression was an independent prognostic factor. The incorporation of REV3L into a nomogram enabled accurate prediction of patient survival. The present study demonstrated a positive correlation between REV3L and effector memory T cells, Th1 cells, and Th17 cells, and a negative correlation with NK CD56bright cells. REV3L-high tumors exhibited enrichment in glycolysis, DNA repair, G2M checkpoint, mitotic spindle, inflammatory response, and MYC target pathways. Silencing REV3L led to the suppression of proliferation, colony formation, lactate production, and glucose uptake, alteration of glycolytic gene expression, and enhancement of cisplatin-induced apoptosis. CONCLUSIONS: The present findings establish a pivotal, context-dependent role for REV3L in BLCA, which is implicated in tumor initiation suppression and aggressive progression promotion through metabolic reprogramming, immune modulation, and therapy resistance. It is evident that REV3L functions as both a robust independent prognostic biomarker and a compelling therapeutic target for BLCA.	bladder
Association of interleukin-6 serum levels with local tumor stage and lymph node metastasis of urothelial carcinoma.	INTRODUCTION: Elevated preoperative interleukin-6 (IL-6) blood levels in urothelial carcinoma (UC) patients undergoing radical cystectomy (RC) have been linked to adverse pathological features. The aim of this prospective study of patients undergoing RC was to analyze whether preoperative IL-6 serum levels (i) correlate with local tumor stage, (ii) are associated with lymph node metastasis, and (iii) are elevated in patients with other oncologic or nononcologic indications for RC. MATERIALS AND METHODS: Patients undergoing RC for oncologic or nononcologic indications were prospectively included. IL-6 serum levels were measured preoperatively. Statistical analysis included Spearman correlation analysis and Receiver Operating Characteristics (ROC) analysis. CLINICALTRIALS: gov: NCT05153694. RESULTS: Between December 2021 and November 2024, 214 patients underwent RC at our department. Preoperative IL-6 serum levels were measured in 169 patients who provided informed consent. In UC patients, IL-6 levels correlated with local tumor stage (r = 0.30, P = 0.001) and higher levels were associated with lymph node metastasis (P = 0.001). The AUC was 0.678 (95% CI 0.58-0.77) and 0.681 (95% CI 0.58-0.79) for non-organ confined tumor growth and lymph node metastasis, respectively. No significant difference in preoperative IL-6 serum levels was observed between UC patients and patients with other oncologic or nononcologic indications for RC. CONCLUSION: This prospective study found that elevated preoperative IL-6 serum levels correlated with local tumor stage and were associated with lymph node metastasis in UC patients undergoing RC. However, IL-6 levels were also elevated in patients with other oncologic or nononcologic indications for RC, underscoring the need for careful interpretation of this marker.	bladder
Targeted Accumulation of Reactive Acrolein via Nanoparticle-embedded Reverse Temperature Hydrogel for Bladder Cancer Treatment.	Rationale: Bladder cancer (BC) frequently recurs after standard surgical resection and is often associated with poor survival outcomes. Local treatment via intravesical instillation of drug in situ is a promising strategy, but its therapeutic efficacy is limited by insufficient retention time and urinary tract obstruction. Methods: We demonstrate that BC exhibits pronounced suppression of acetylpolyamine oxidase (PAOX) compared to normal tissues, as evidenced by multi-platform analysis of patient-derived clinical specimens and GEO database. The PAOX deficiency drives pathological polyamine accumulation in BC cells, uncovering a novel metabolic target with therapeutic implications. Thus, we engineered a novel intravesical instillation system that combines PAOX/targeting peptide-conjugated nanoparticles, synergistically boosting reactive acrolein synthesis while blocking detoxification to induce lethal carbonyl stress, and reverse temperature hydrogels, ensuring liquid dispersion for full bladder coverage during instillation, followed by in situ gelation to prolong nanoparticle retention. Results: In vitro and in vivo results showed that this nanoparticle-embedded hydrogel disrupt redox homeostasis by amplifying lethal carbonyl stress via mitochondrial dysfunction, lipid peroxidation and DNA damage. Remarkably, acrolein binding to GAPDH promotes its nuclear translocation and upregulation of the tumor suppressor protein P53, facilitating apoptosis. Conclusion: This innovative strategy enhances reactive acrolein accumulation by targeting tumor-specific metabolic vulnerabilities, inducing multifaceted cell death for the BC treatment.	bladder
Cerium oxide-embedded gold nanoparticles loaded with astragaloside IV for bladder cancer therapy.	In bladder cancer, metabolic dysregulation of reactive oxygen species (ROS) promotes malignant transformation through oxidative DNA damage while concurrently activating pro-survival pathways such as NF-κB. To address this, we developed a synergistic therapeutic platform by incorporating gold nanoparticles into cerium oxide nanostructures (Au/CeO₂) with enhanced antioxidant activity, followed by loading with astragaloside IV (Au/CeO₂@As). The core-shell structured Au/CeO₂@As nanocomposites demonstrated remarkable pro-apoptotic effects, exhibiting a 5.11-fold increase in apoptosis induction compared to free astragaloside IV alone. Subsequent cell proliferation assays confirmed the system's ability to effectively inhibit tumor cell migration and proliferation. Mechanistic investigations through qPCR and Western blot analyses revealed that Au/CeO₂@As mediates its antitumor effects through coordinated regulation of the STAT3 and NF-κB signaling pathways, leading to significant tumor cell damage. Importantly, the Au/CeO₂@As nanocomposites did not exhibit significant cytotoxicity while demonstrating excellent therapeutic efficacy. These findings collectively establish Au/CeO₂@As as a highly promising nanotherapeutic candidate for bladder cancer treatment, offering both targeted ROS modulation and specific pathway regulation capabilities.	bladder
Thrombospondin-4 drives lymphangiogenesis through cooperation with VEGF-C in human bladder cancer.	Introduction: Bladder cancer (BLCA) is the second most common malignancy of the male urinary tract, with frequent metastasis to pelvic lymph nodes and, in advanced stages, to distant organs such as the lungs, liver, and bones. Thrombospondin-4 (TSP4), an extracellular matrix protein, has been implicated in cell adhesion, migration, proliferation, and cytoskeletal regulation. However, its role in lymphatic metastasis remains poorly understood. Methods: TSP4 mRNA and protein levels were assessed by RT-qPCR and Western blot analyses. Lymphangiogenesis and lymphatic endothelial cell (LEC) migration were respectively evaluated using tube-formation and transwell assays. The Cancer Genome Atlas (TCGA)-BLCA datasets were analyzed to compare expressions of TSP family members across lymph node metastasis stages. A popliteal lymph node metastasis model was employed to isolate lymph node-tropic BLCA cell lines. Results: TSP4 expression was positively associated with lymph node metastasis stages in BLCA tissues. In vitro, conditioned medium (CM) from 5637 and T24 cells promoted LEC recruitment and tube formation, while a TSP4-neutralizing antibody impaired LEC migration without affecting tube formation. Mechanistically, TSP4 enhanced LEC migration by upregulating intercellular cell adhesion molecule (ICAM)-1 and activating the integrin αvβ3/focal adhesion kinase (FAK)/extracellular signal-regulated kinase (ERK) pathway. Notably, TSP4 also induced vascular endothelial growth factor C (VEGF-C) expression in BLCA cells. Both TSP4 and VEGF-C were upregulated in lymph node-tropic BLCA cell lines, with a positive correlation observed in TCGA-BLCA datasets. VEGF-C neutralization abolished CM-induced LEC tube formation, highlighting the role of the TSP4/VEGF-C axis in lymphangiogenesis. Conclusions: This is the first study to demonstrate that BLCA-derived TSP4 cooperates with VEGF-C to promote lymphangiogenesis within the tumor microenvironment. These findings suggest that TSP4 could serve as a potential therapeutic target for preventing lymphatic metastasis in human BLCA.	bladder
Sorafenib inhibits myeloid-derived suppressor cell infiltration in canine transitional cell carcinoma.	Myeloid-derived suppressor cells (MDSCs)-immature cells with immunosuppressive properties-are promising therapeutic targets for cancer immunotherapy. However, established therapies targeting MDSCs remain lacking, and novel molecules are needed to regulate MDSCs. Sorafenib, a tyrosine kinase (TRK) inhibitor, suppresses MDSCs. As TRKs regulate chemokine production, we hypothesized that sorafenib inhibits MDSCs by regulating chemokine production. This study aimed to investigate the effect of sorafenib on MDSCs and its underlying mechanism in canine transitional cell carcinoma (cTCC). Sorafenib reduced the number of MDSCs and downregulated CX3CL1 expression in the tumor tissues of cTCC-transplanted mice. Vascular endothelial growth factor A (VEGF-A) and platelet derived growth factor-BB (PDGF-BB) recombinant protein, the target axis of sorafenib, increased CX3CL1 expression in cTCC cell line. Furthermore, a positive correlation was observed between urinary levels of CX3CL1 and VEGF-A in cTCC cases. These results indicated that VEGF-A signaling can regulate CX3CL1 expression. Next, we analyzed whether CX3CL1 accelerates MDSC infiltration. MDSCs expressed CX3CR1, the receptor for CX3CL1, and migrated toward recombinant CX3CL1 protein in a dose-dependent manner. In a cTCC-transplanted mouse model, CX3CL1 depletion or treatment with a CX3CR1 inhibitor showed anti-tumor effects and reduced MDSCs in the tumor tissue. Overall, our results indicated that CX3CL1 promotes MDSC infiltration, and the CX3CL1/CX3CR1 axis could be a therapeutic target for regulating MDSCs in dogs with cTCC.	bladder
Evaluating the Impact of Febuxostat on 5-Aminolevulinic Acid-Based Photodynamic Therapy in Bladder Cancer Cell Lines.	BACKGROUND: Bladder cancer (BC) is a prevalent malignancy worldwide, with significant challenges in recurrence management following conventional treatments. This study investigates the potential of Febuxostat, an established xanthine oxidase inhibitor, to enhance the efficacy of photodynamic therapy (PDT) utilizing 5-aminolevulinic acid (5-ALA) in bladder cancer cell lines T24 and 5637. METHODS: In this in vitro study, we evaluated the effect of 5-ALA, Febuxostat and 5-ALA- Febuxostat combination therapy in T24 and 5637 cell lines as representatives of human bladder cancer. The assessment includes scratch-wound assay, colony formation assay, ROS measurement, flow cytometric analysis of apoptosis and DNA cell cycle, real-time PCR (BAX/BCL2, E-cadherin, N-cadherin, HIF1α and VEGFC genes). RESULTS: Our findings demonstrate that co-administration of Febuxostat significantly increases ROS output compared to ALA treatment alone (p-value ≤ 0.05), leading to enhanced cytotoxicity and apoptosis. Flow cytometric analyses revealed elevated apoptosis rates in combination treatment groups, and cell cycle assessments indicated a preferential sub-G1 phase arrest associated with the enhanced apoptotic response (P Value = 0.03). Additionally, gene expression profiling showed alterations in key apoptotic markers (BAX/BCL2), with an upregulation of pro-apoptotic genes and a downregulation of anti-apoptotic factors and increase E-Cadherin/N-Cadherin in response to Febuxostat-enhanced PDT (P Value>0.05). CONCLUSION: These results indicate that Febuxostat effectively potentiates the photodynamic effects of ALA in bladder cancer cells, promising a novel therapeutic strategy that warrants further exploration.	bladder
Pharmacokinetics of UGN‑102, an investigational mitomycin‑containing reverse thermal gel for the treatment of non-muscle invasive bladder cancer.	PURPOSE: To evaluate the pharmacokinetic properties of UGN-102, a mitomycin-containing reverse thermal gel. METHODS: Twelve patients with NMIBC received 6 once-weekly intravesical instillations of UGN-102 (BL004: 120 mg mitomycin [n = 6]; BL005: 75 mg mitomycin [n = 6]). Plasma samples for determination of pharmacokinetic (PK) parameters were collected up to 6 h following instillation. RESULTS: In BL004, mean C(max) was 20.39 ng/mL, and median was 16.10 ng/mL (range 4.00-40.40), 100-10-fold lower than reported myelosuppression toxic level (RMTL); and median T(max) was 1.5 h. Mean AUC(0-6) was 56.23 ng·h/mL and mean apparent terminal half-life (t(1/2)) was 49 min. The highest observed C(max) (40.40 ng/mL) was 59-fold and 13-fold lower than C(max) following IV 30 mg or 10 mg mitomycin, respectively, and 10-fold lower than the RMTL. Maximum measured urine concentration was 635 µg/mL. In BL005, mean C(max) was 2.27 ng/mL, 181-fold lower than the RMTL; mean T(max) was 1.95 h and mean AUC(0-6) was 5.69 ng·h/mL. At 4-6 h post intravesical instillation, mitomycin concentrations in urine were either below or approaching the lower level of quantification (< 0.250 µg/mL) in 5/6 patients. In the remaining patient, the measurable urine concentrations over the 6-hour period suggest dwell time was > 6 h post-instillation, possibly due to the tumor location restricting urine flow. However systemic exposure was < 4 ng/mL, 100-fold lower than the RMTL. CONCLUSIONS: Intravesical instillation of UGN-102 results in low-level systemic absorption of mitomycin, with C(max) values considerably lower than those following IV administration and those associated with myelosuppression. STUDY REGISTRATION: BL004: NCT02307487; BL005: NCT03558503.	bladder